3KYC	Ligase	date	Dec 05, 2009
title	Human Sumo E1 Complex With A Sumo1-Amp Mimic
authors	C.D.Lima
compound		source
Molecule: Sumo-Activating Enzyme Subunit 1 Chain: A Synonym: Ubiquitin-Like 1-Activating Enzyme E1a Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Aos1, Sae1, Sua1, Uble1a Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21 De3 Cp Ril Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet-15b
Molecule: Sumo-Activating Enzyme Subunit 2 Chain: B Synonym: Ubiquitin-Like 1-Activating Enzyme E1b, Anthracycl Associated Resistance Arx; Ec: 6.3.2.- Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Hrihfb2115, Sae2, Uba2, Uble1b Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21 De3 Cp Ril Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet28b
Molecule: Small Ubiquitin-Related Modifier 1 Chain: D Fragment: Unp Residues 1-97 Synonym: Sumo-1, Sentrin, Ubiquitin-Like Protein Smt3c, Smt 3, Ubiquitin-Homology Domain Protein Pic1, Ubiquitin-Like P Ubl1, Gap-Modifying Protein 1, Gmp1; Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Oksw-Cl.43, Smt3c, Smt3h3, Sumo1, Ubl1 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21 De3 Cp Ril Expression_system_vector_type: Plasmid Expression_system_plasmid: Ptxb1
symmetry	Space Group: P 21 21 21	R_factor 0.191 R_Free 0.250
crystal cell	length a length b length c angle alpha angle beta angle gamma 59.174 133.365 159.656 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.45 Å
ligand	JZU, ZN	enzyme	Ligase E.C.6.3.2 BRENDA
Gene Ontology	Chain Function Process Component A ubiquitin activating enzyme ... enzyme activator activity B D
Primary reference	Active site remodelling accompanies thioester bond formation in the SUMO E1., Olsen SK, Capili AD, Lu X, Tan DS, Lima CD, Nature. 2010 Feb 18;463(7283):906-12. PMID:20164921

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (161 Kb) [Save to disk] Biological Unit Coordinates (3kyc.pdb1.gz) 153 Kb LPC: Ligand-Protein Contacts for 3KYC CSU: Contacts of Structural Units for 3KYC Structure Factors (1108 Kb) Retrieve 3KYC in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3KYC from S2C, [Save to disk] Re-refined 3kyc structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3KYC in 3D

Proteopedia, because life has more than 2D. On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure. On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.

Visual 3D analysis of 3KYC

Ramachandran plot from PDBSum

Structure-derived information

Electron Density related parameters from EDS Electron Density Server, at Upsala Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 3KYC, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3kyc_D] [3kyc_B] [3kyc] [3kyc_A] SWISS-PROT database: Domain organization of by SWISSPFAM Domain found in 3KYC: [UBQ ] by SMART

Other resources with information on 3KYC

Community annotation for 3KYC at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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